PROJECT SUMMARY The intestine displays striking structural and functional variability along its length, allowing for compartmentalization of distinct processes involved in absorption of nutrients and host defense. Regional differences within the intestine are also evident in numerous gastrointestinal (GI) pathologies, such as ileocolitis which is the most common forms of Crohn's disease, and necrotizing enterocolitis, both of which largely affect the distal bowel. The underlying causes of regionality in these GI diseases and others are not well understood, and therapies to restore structure and function to severely damaged or surgically resected diseased tissue are critically needed. Specific subsets of secretory epithelial cells, which play critical roles in digestion and host defense, vary in distribution across the length of the intestine, likely supporting localized functional demand during homeostasis. Damage or disease, however, can radically alter the distributions of these cell types. For example, hyperplasia of secretory tuft and goblet cells following parasite infection is a key component of the tissue remodeling process that expels the pathogen. The cellular and molecular mechanisms that set the normal distribution of secretory cells across the small intestine, and those that disturb secretory patterns in response to parasite infection, are not known. Here, I will test the hypothesis that regional subpopulations of intestinal stem cells (ISCs) that I have identified in my preliminary studies are programmed with a regional gene expression signature termed regional identity (rID), that contributes to the specialized distribution of secretory cells across the small intestine. To identify molecular mechanisms by which regional ISCs control secretory cell distribution during homeostasis, I will analyze single cell RNA sequencing data to define rID transcripts relevant for the control of secretory differentiation, and I will use genetic tools to manipulate these transcripts in ISCs in vitro. I will then use microscopy and sequencing approaches to define cellular mechanisms that increase the relative ratio of tuft and goblet cells in a parasite infection model. Collectively, these experiments will elucidate mechanisms by which regional ISCs maintain specialized domains of secretory cells, and the relevance of this organization for host defense against parasites, which represent one of the most common human infections in the world. The results of this study have clinical implications for restoring regional function that has been compromised by enteric infection, gastrointestinal disease, and bowel resection.